information about a bead More...

#include <bead.h>

Inheritance diagram for votca::csg::Bead:

Collaboration diagram for votca::csg::Bead:

[legend]

Public Types
enum	Symmetry { spherical = 1 , ellipsoidal = 3 }
	get the symmetry of the bead More...

Public Member Functions
	~Bead () override=default

const Index &	getResnr () const

virtual const double &	getQ () const

virtual void	setQ (const double &q)

Symmetry	getSymmetry () const

void	setVel (const Eigen::Vector3d &r)

const Eigen::Vector3d &	getVel () const

void	setU (const Eigen::Vector3d &u)
	set first orientation (normal vector) vector of bead

const Eigen::Vector3d &	getU () const
	get first orientation (normal vector) vector of bead

void	setV (const Eigen::Vector3d &v)
	set second orientation vector of bead

const Eigen::Vector3d &	getV () const
	get second orientation vector of bead

void	setW (const Eigen::Vector3d &w)
	set third orientation vector of bead

const Eigen::Vector3d &	getW () const
	get third orientation vector of bead

Eigen::Vector3d &	Vel ()

Eigen::Vector3d &	U ()

Eigen::Vector3d &	V ()

Eigen::Vector3d &	W ()

Eigen::Vector3d &	F ()

void	setF (const Eigen::Vector3d &bead_force)

const Eigen::Vector3d &	getF () const
	get the force acting on the bead

bool	HasVel () const noexcept

bool	HasF () const noexcept

bool	HasU () const noexcept

bool	HasV () const noexcept

bool	HasW () const noexcept

void	HasVel (bool b)

void	HasF (bool b)

void	HasU (bool b)

void	HasV (bool b)

void	HasW (bool b)

const std::vector< Index > &	ParentBeads ()

void	ClearParentBeads ()
	Clears out all parent beads.

void	AddParentBead (Index parent_bead_id)
	Adds the id of a parent bead.

Public Member Functions inherited from votca::csg::BaseBead
virtual	~BaseBead ()=default

Index	getId () const noexcept
	Gets the id of the bead.

void	setId (const Index &id) noexcept
	Sets the id of the bead.

std::string	getName () const
	Gets the name of the bead.

void	setName (std::string name)
	Sets the name of the bead.

void	setMoleculeId (const Index &molecule_id) noexcept
	assign the bead to a molecule with the provided id

Index	getMoleculeId () const noexcept
	Get the id of the molecule the bead is a part of, if the molecule id has not been set return topology_constants::unassigned_molecule_id.

virtual const std::string	getType () const noexcept

virtual void	setType (const std::string &type) noexcept

std::string	getElement () const noexcept
	Returns the element type of the bead.

virtual const double &	getMass () const noexcept

virtual void	setMass (const double &m) noexcept

virtual void	setPos (const Eigen::Vector3d &bead_position)

virtual const Eigen::Vector3d &	getPos () const

virtual Eigen::Vector3d &	Pos ()

virtual const Eigen::Vector3d &	Pos () const

bool	HasPos () const noexcept

void	HasPos (const bool &true_or_false) noexcept

Protected Member Functions
	Bead (Index id, std::string type, Symmetry symmetry, std::string name, Index resnr, double m, double q)
	constructor

Protected Member Functions inherited from votca::csg::BaseBead
	BaseBead ()=default

Protected Attributes
std::vector< Index >	parent_beads_

Symmetry	symmetry_

double	charge_

Index	residue_number_

Eigen::Vector3d	velocity_

Eigen::Vector3d	bead_force_

Eigen::Vector3d	u_

Eigen::Vector3d	v_

Eigen::Vector3d	w_

bool	bead_velocity_set_

bool	bU_

bool	bV_

bool	bW_

bool	bead_force_set_

Protected Attributes inherited from votca::csg::BaseBead
std::string	type_ = tools::topology_constants::unassigned_bead_type

Index	id_ = tools::topology_constants::unassigned_residue_id

Index	molecule_id_ = tools::topology_constants::unassigned_molecule_id

std::string	element_symbol_ = tools::topology_constants::unassigned_element

TOOLS::Name	name_

double	mass_ = 0.0

Eigen::Vector3d	bead_position_

bool	bead_position_set_ = false

Friends
class	Topology

class	Molecule

Detailed Description

information about a bead

The Bead class describes an atom or a coarse grained bead. It stores information like the id, the name, the mass, the charge and the residue it belongs to. The coordinates are stored in the configuration class.

Todo

change resnr to pointer

make sure bead belongs to topology

Definition at line 50 of file bead.h.

Member Enumeration Documentation

◆ Symmetry

enum votca::csg::Bead::Symmetry

get the symmetry of the bead

Returns the number of unique axis of the bead, it can be 1 for a spherical bead 3 for an ellipsoidal bead 2 (currently not used), could be disk like particle

Returns: bead symmetry

Enumerator
spherical
ellipsoidal

Definition at line 85 of file bead.h.

Constructor & Destructor Documentation

◆ ~Bead()

votca::csg::Bead::~Bead ( )

overridedefault

destructor

◆ Bead()

votca::csg::Bead::Bead	(	Index	id,
		std::string	type,
		Symmetry	symmetry,
		std::string	name,
		Index	resnr,
		double	m,
		double	q )

inlineprotected

constructor

Definition at line 296 of file bead.h.

Member Function Documentation

◆ AddParentBead()

void votca::csg::Bead::AddParentBead ( Index parent_bead_id )

inline

Adds the id of a parent bead.

Definition at line 275 of file bead.h.

◆ ClearParentBeads()

void votca::csg::Bead::ClearParentBeads ( )

inline

Clears out all parent beads.

Definition at line 270 of file bead.h.

◆ F()

Eigen::Vector3d & votca::csg::Bead::F ( )

inline

direct access (read/write) to the force of the bead

Returns: reference to force

Definition at line 210 of file bead.h.

◆ getF()

const Eigen::Vector3d & votca::csg::Bead::getF ( ) const

inline

get the force acting on the bead

Forces have to be provided by the trajectory. If beads are mapped, forces of coarse-grained beads are also calculated.

Returns: force on bead

Definition at line 361 of file bead.h.

◆ getQ()

virtual const double & votca::csg::Bead::getQ ( ) const

inlinevirtual

get the charge of the bead

Returns: - base bead charge

Definition at line 67 of file bead.h.

◆ getResnr()

const Index & votca::csg::Bead::getResnr ( ) const

inline

get the residu number of the bead

Returns: residue id

Definition at line 61 of file bead.h.

◆ getSymmetry()

Symmetry votca::csg::Bead::getSymmetry ( ) const

inline

Definition at line 86 of file bead.h.

◆ getU()

const Eigen::Vector3d & votca::csg::Bead::getU ( ) const

inline

get first orientation (normal vector) vector of bead

Non-spherical beads (symmetry 3) have a internal coordinates system and the axes are denoted as u, v and w. Currently the non-spherical mapping is hardcoded and the axis u is calculated by the eigenvector with the lowest eigenvector of the mapped beads and has the meaning of a normal vector if the reference beads have a disc like shape. The sign of the normal vector is determined in combination with the vectors v and w to build up a right handed (??) coordinate system.

Returns: bead orientation u

Definition at line 331 of file bead.h.

◆ getV()

const Eigen::Vector3d & votca::csg::Bead::getV ( ) const

inline

get second orientation vector of bead

Non-spherical beads (symmetry 3) have a internal coordinates system and the axes are denoted as u, v and w. Currently the non-spherical mapping is hardcoded and the axis v is the vector which connects first and second reference atom in the mapping (only orthogonal component to u).

Returns: bead orientation u

Definition at line 341 of file bead.h.

◆ getVel()

const Eigen::Vector3d & votca::csg::Bead::getVel ( ) const

inline

get the velocity of the bead

Returns: bead velocity

Definition at line 320 of file bead.h.

◆ getW()

const Eigen::Vector3d & votca::csg::Bead::getW ( ) const

inline

get third orientation vector of bead

Non-spherical beads (symmetry 3) have a internal coordinates system and the axes are denoted as u, v and w. Currently the non-spherical mapping is hardcoded and the axis w is orthogonal to u and v.

Returns: bead orientation w

Definition at line 374 of file bead.h.

◆ ParentBeads()

const std::vector< Index > & votca::csg::Bead::ParentBeads ( )

inline

If it is a mapped beads, returns te bead id the cg bead was created from

Returns: vector of bead ids of reference atoms

Definition at line 265 of file bead.h.

◆ setF()

void votca::csg::Bead::setF ( const Eigen::Vector3d & bead_force )

inline

set force acting on bead

Parameters

bead_force force

Definition at line 356 of file bead.h.

◆ setQ()

virtual void votca::csg::Bead::setQ ( const double & q )

inlinevirtual

set the charge of the base bead

Parameters

[in] q - base bead position

Definition at line 73 of file bead.h.

◆ setU()

void votca::csg::Bead::setU ( const Eigen::Vector3d & u )

inline

set first orientation (normal vector) vector of bead

see getU for details

Parameters

u	bead orientation u

Definition at line 326 of file bead.h.

◆ setV()

void votca::csg::Bead::setV ( const Eigen::Vector3d & v )

inline

set second orientation vector of bead

see getV for details

Parameters

v	bead orientation v

Definition at line 336 of file bead.h.

◆ setVel()

void votca::csg::Bead::setVel ( const Eigen::Vector3d & r )

inline

set the velocity of the bead

Parameters

r	bead velocity

Definition at line 315 of file bead.h.

◆ setW()

void votca::csg::Bead::setW ( const Eigen::Vector3d & w )

inline

set third orientation vector of bead

see getW for details

Parameters

w	bead orientation w

Definition at line 346 of file bead.h.

◆ U()

Eigen::Vector3d & votca::csg::Bead::U ( )

inline

direct access (read/write) to orientation u of the bead

Returns: reference to u

Definition at line 183 of file bead.h.

◆ V()

Eigen::Vector3d & votca::csg::Bead::V ( )

inline

direct access (read/write) to the orientation v of the bead

Returns: reference to v

Definition at line 192 of file bead.h.

◆ Vel()

Eigen::Vector3d & votca::csg::Bead::Vel ( )

inline

direct access (read/write) to the velocity of the bead

Returns: reference to velocity

Definition at line 173 of file bead.h.

◆ W()

Eigen::Vector3d & votca::csg::Bead::W ( )

inline

direct access (read/write) to the orientation w of the bead

Returns: reference to w

Definition at line 201 of file bead.h.

Friends And Related Symbol Documentation

◆ Molecule

friend class Molecule

friend

Definition at line 312 of file bead.h.

◆ Topology

friend class Topology

Eigen::Vector3d votca::csg::Bead::w_

protected

Definition at line 287 of file bead.h.

The documentation for this class was generated from the following file:

csg/include/votca/csg/bead.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ Symmetry

Constructor & Destructor Documentation

◆ ~Bead()

◆ Bead()

Member Function Documentation

◆ AddParentBead()

◆ ClearParentBeads()

◆ F()

◆ getF()

◆ getQ()

◆ getResnr()

◆ getSymmetry()

◆ getU()

◆ getV()

◆ getVel()

◆ getW()

◆ HasF() [1/2]

◆ HasF() [2/2]

◆ HasU() [1/2]

◆ HasU() [2/2]

◆ HasV() [1/2]

◆ HasV() [2/2]

◆ HasVel() [1/2]

◆ HasVel() [2/2]

◆ HasW() [1/2]

◆ HasW() [2/2]

◆ ParentBeads()

◆ setF()

◆ setQ()

◆ setU()

◆ setV()

◆ setVel()

◆ setW()

◆ U()

◆ V()

◆ Vel()

◆ W()

Friends And Related Symbol Documentation

◆ Molecule

◆ Topology

Member Data Documentation

◆ bead_force_

◆ bead_force_set_

◆ bead_velocity_set_

◆ bU_

◆ bV_

◆ bW_

◆ charge_

◆ parent_beads_

◆ residue_number_

◆ symmetry_

◆ u_

◆ v_

◆ velocity_

◆ w_